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Chaining Algorithms for Alignment of Draft Sequence [chapter]

Mukund Sundararajan, Michael Brudno, Kerrin Small, Arend Sidow, Serafim Batzoglou
2004 Lecture Notes in Computer Science  
In this paper we propose a chaining method that can align a draft genomic sequence against a finished genome.  ...  The algorithm is tested on a whole genome alignment of seven yeast species.  ...  Draft Sequence Alignment The goal of the draft sequence alignment problem is to map the sections of the finished sequence (Sequence 1) to sections of the draft contigs (Sequence 2).  ... 
doi:10.1007/978-3-540-30219-3_28 fatcat:rimhvmuyunf6jhwknce6lmplrq

AVID: A Global Alignment Program

N. Bray
2002 Genome Research  
The method is designed to be fast, memory efficient, and practical for sequence alignments of large genomic regions up to megabases long.  ...  To this end, we have established a format for the representation of alignments and methods for their comparison. These formats and methods should be useful for future studies.  ...  Some of the sequence data used to benchmark the alignment programs were generated by the NIH Intramural Sequencing Center (www.nisc.nih.gov).  ... 
doi:10.1101/gr.789803 pmid:12529311 pmcid:PMC430967 fatcat:7gnoeoimpjf5foh5236haowj5q

CoCoNUT: an efficient system for the comparison and analysis of genomes

Mohamed I Abouelhoda, Stefan Kurtz, Enno Ohlebusch
2008 BMC Bioinformatics  
similarity among multiple genomic sequences and aligning them, (2) comparing two draft or multi-chromosomal genomes, (3) locating large segmental duplications in large genomic sequences, and (4) mapping  ...  This area of research is driven by the large number of sequenced genomes and heavily relies on efficient algorithms and software to perform pairwise and multiple genome comparisons.  ...  We would like to thank the anonymous reviewers for valuable comments on a previous version of the article.  ... 
doi:10.1186/1471-2105-9-476 pmid:19014477 pmcid:PMC3224568 fatcat:mr5dvlfk3jgxjoihuk5nojomxi

An applications-focused review of comparative genomics tools: Capabilities, limitations and future challenges

P. Chain
2003 Briefings in Bioinformatics  
We note that genome alignments are important for many things, only one of which is pathogen detection.  ...  Understanding gene function, gene regulation, gene networks, phylogenetic studies and other aspects of evolution all depend on accurate nucleic acid and protein sequence alignment.  ...  Thanks also to Burkhard Morgenstern for his suggestions improving the description of DIALIGN.  ... 
doi:10.1093/bib/4.2.105 pmid:12846393 fatcat:3p5ybliqe5earn3hz4bmatuljy

Multiple whole-genome alignments without a reference organism

I. Dubchak, A. Poliakov, A. Kislyuk, M. Brudno
2009 Genome Research  
Acknowledgments We thank Rotem Sorek, Adrian Dalca, and Nilgun Donmez for critical readings of this manuscript. We are also grateful to the anonymous reviewers for their feedback.  ...  This work was also supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.  ...  Designing a progressive nonreferenced framework for aligning both finished and draft genomes is an important future goal, as many genomes sequenced today are left in draft form.  ... 
doi:10.1101/gr.081778.108 pmid:19176791 pmcid:PMC2665786 fatcat:szo6g3gxcfcs5jazhdzgkeaaby

Hapo-G, Haplotype-Aware Polishing Of Genome Assemblies [article]

Jean-Marc Aury, Benjamin Istace
2020 bioRxiv   pre-print
then, using efficient algorithms, provide high quality assemblies in terms of contiguity and completeness of repetitive regions.  ...  Single-molecule sequencing technologies have recently been commercialized by Pacific Biosciences and Oxford Nanopore with the promise of sequencing long DNA fragments (kilobases to megabases order) and  ...  All reliable chains of variants were searched in the alignment results and a given chain was validated only if all its variants were found in a perfect match and on the same genomic sequence.  ... 
doi:10.1101/2020.12.14.422624 fatcat:jdvdm2yizvcuhdxpp7cq44xjzi

Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads

Jean-Marc Aury, Benjamin Istace
2021 NAR Genomics and Bioinformatics  
then, using efficient algorithms, provide high quality assemblies in terms of contiguity and completeness of repetitive regions.  ...  Single-molecule sequencing technologies have recently been commercialized by Pacific Biosciences and Oxford Nanopore with the promise of sequencing long DNA fragments (kilobases to megabases order) and  ...  ACKNOWLEDGEMENTS The authors thank Pierre Peterlongo for his support and advice with discoSNP and his proofreading of the manuscript. FUNDING  ... 
doi:10.1093/nargab/lqab034 pmid:33987534 pmcid:PMC8092372 fatcat:sjwim42uojcy3lshofuqfskwom

Fast and sensitive multiple alignment of large genomic sequences

Michael Brudno, Michael Chapman, Berthold Göttgens, Serafim Batzoglou, Burkhard Morgenstern
2003 BMC Bioinformatics  
Herein, we present CHAOS, a novel algorithm for rapid identification of chains of local pair-wise sequence similarities.  ...  One way of combining speed and sensitivity is to use an anchored-alignment approach. In a first step, a fast search program identifies a chain of strong local sequence similarities.  ...  Do for help with CHAOS development, Nadine Werner for assistance with the manuscript, and Inna Dubchak for valuable conversations during this study.  ... 
doi:10.1186/1471-2105-4-66 pmid:14693042 pmcid:PMC521198 fatcat:afy6qa6blzhxrfdq3fl7u67asm

Reconstructing B-cell receptor sequences from short-read single-cell RNA sequencing with BRAPeS

Shaked Afik, Gabriel Raulet, Nir Yosef
2019 Life Science Alliance  
We present BRAPeS ("BCR Reconstruction Algorithm for Paired-end Single cells" ), an algorithm for reconstructing BCRs from short-read paired-end single-cell RNA sequencing.  ...  However, to uncover the latter, further reconstruction of the BCR sequence is needed.  ...  The BRAPeS algorithm has several steps, performed separately for each chain in each cell: 1.  ... 
doi:10.26508/lsa.201900371 pmid:31451449 pmcid:PMC6709718 fatcat:jrqb27yjqvcuhn4p5fzfu7wmcq

CSA: An efficient algorithm to improve circular DNA multiple alignment

Francisco Fernandes, Luísa Pereira, Ana T Freitas
2009 BMC Bioinformatics  
This algorithm identifies the largest chain of non-repeated longest subsequences common to a set of circular mitochondrial DNA sequences.  ...  All the sequences are then rotated and made linear for multiple alignment purposes.  ...  This project was supported by the ARN project -Algorithms for the identification of genetic Regulatory Networks (PTDC/EIA/67722/2006) from the Portuguese Science Foundation (FCT).  ... 
doi:10.1186/1471-2105-10-230 pmid:19627599 pmcid:PMC2722656 fatcat:u7vqib7g6bcndb5xfbe2gpeppi

GenomeVISTA—an integrated software package for whole-genome alignment and visualization

Alexandre Poliakov, Justin Foong, Michael Brudno, Inna Dubchak
2014 Computer applications in the biosciences : CABIOS  
Our VISTA family of tools for comparative genomics, based on algorithms for pairwise and multiple alignments of genomic sequences and whole-genome assemblies, has become one of the standard techniques  ...  With the ubiquitous generation of complete genome assemblies for a variety of species, efficient tools for whole-genome alignment along with user-friendly visualization are critically important.  ...  ACKNOWLEDGEMENTS The authors are grateful to all VISTA developers, collaborators and users for support and suggestions for its ongoing development.  ... 
doi:10.1093/bioinformatics/btu355 pmid:24860159 pmcid:PMC4155257 fatcat:yhc4w7oh5vacvjglhnyt5aivye

PILER-CR: Fast and accurate identification of CRISPR repeats

Robert C Edgar
2007 BMC Bioinformatics  
Sequencing of prokaryotic genomes has recently revealed the presence of CRISPR elements: short, highly conserved repeats separated by unique sequences of similar length.  ...  We validate the algorithm by manual curation and by comparison with published surveys of these repeats, finding that PILER-CR has both high sensitivity and high specificity.  ...  The author is grateful to Viktor Kunin for suggesting that PILER could be adapted to find CRISPR repeats and for helpful feedback on early versions of the program.  ... 
doi:10.1186/1471-2105-8-18 pmid:17239253 pmcid:PMC1790904 fatcat:hvyd23oamrbhpbyggzmc5t7ygq

Bioinformatics Support of Genome Sequencing Projects [chapter]

Xiaoqiu Huang
2004 Bioinformatics - From Genomes to Drugs  
The structure of a genome is a linear sequence of nucleotides. Determination of the sequence of a genome lays the foundation for understanding biology at the molecular level.  ...  With the current biotechnology, it is a challenging task to determine the sequence of a genome. A sequencing machine can read the sequence of a piece of DNA for up to 1000 bp (base pairs).  ...  Acknowledgments I would like to thank Thomas Lengauer for many helpful suggestions on the presentation of this Chapter.  ... 
doi:10.1002/3527601481.ch10 fatcat:tlyqqmuoc5dgppngwhnv22ccjy

A Python script to merge Sanger sequences

Cen Chen, Bingguo Lu, Xiaofang Huang, Chuyun Bi, Lili Zhao, Yunzhuo Hu, Xuanyang Chen, Shiqiang Lin, Kai Huang
2021 PeerJ  
The script offers a simple and free method for merging Sanger sequences and is useful for gene cloning.  ...  The script utilizes the overlapping regions within the tandem Sanger sequences to merge the Sanger sequences.  ...  Besides, using "EMBOSS" "needle", our algorithm can align tandemly arranged Sanger sequences and calculate the boundary of sequences to merge, potentially minimizing the influence of repeated sequences  ... 
doi:10.7717/peerj.11354 pmid:33987023 pmcid:PMC8086567 fatcat:hxozygfv5rhwtndpjvbzdccsyi

SeedsGraph: an efficient assembler for next-generation sequencing data

Chunyu Wang, Maozu Guo, Xiaoyan Liu, Yang Liu, Quan Zou
2015 BMC Medical Genomics  
We condense each group of reads to a chain of seeds, which is a kind of substring with reads aligned, and then build a graph accordingly.  ...  The result shows that our algorithm is efficient and feasible for a large set of reads such as in next-generation sequencing technology.  ...  MG is supported by the Natural Science Foundation of China  ... 
doi:10.1186/1755-8794-8-s2-s13 pmid:26044652 pmcid:PMC4460749 fatcat:tn2vo42b6ff53hqconulsz7tby
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